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Anthropology 2235A/B
Eldon Molto

Anthro Notes Sept. 27/12 Lec. 4 - Nuclear DNA analysis history: RFLP technique developed by Jeffreys in 1988 was implemented quickly in the UK, US, and Canada. US private (cell mark 1988) and public (FBI 1988) labs developed DNA divisions. In Canada there were government labs only. This is a key difference in the delivery of DNA forensics between Canada, UK, and US. The first key trial was in spring 1989 following a voir dire hearing. It was the R. vs. McNally case. John Wayne from McMaster University, representing the RCMP lab, reported a match between McNally and samples recovered from a 68-year-old woman. McNally, upon hearing the random match probability results (1 in several billion), changed his plea from not-guilty to guilty. The first major trial in Ontario was R. vs. Johnny Terceira in Oct. 1992. Exonerations based on DNA lead to the innocence project in the US and the association in defence of the wrongfully convicted in Canada. Labs today would be based on SNPs if things could be restarted because 19 SNPs can provide a match probability as high as 1 in 10 billion. As of 2008, CODIS contained over 5 million offender and forensic profiles and had over 45,000 hits. - History of mitochondrial genome: Since the early 1970s, it was realized that DNA was present in the mitochondria of human cells. Mitochondria have a clonal mode of inheritance and it was argued that they evolved as a symbiotic organelle within the eukaryotic cell to produce energy (endo-symbiotic hypothesis). Following the sequencing breakthrough by Fred Sanger in the 1970s, a Cambridge team completely sequenced the mitochondrial genome in 1981. Initially called the Anderson sequence, it was changed to the Cambridge reference sequence (CRS) with a few modifications. It first gained prominence in evolutionary anthropology studies in the mid-1980s, particularly in terms of a new hypothesis on the origins of modern homo sapiens. This hypothesis called out of Africa posited that homo sapiens sapiens (modern humans) evolved from early sapiens between 100 and 200,000 years ago. The use of mtDNA in ancient DNA research in the 1980s focused on its suitability for ancient tissues. This paved the way for work in forensics where degraded tissues are encountered (cold cases, low product). The first mitochondrial DNA forensic cases occurred in the US and UK in the mid-1990s. The first case in Canada was R. vs. Murrin following a voir dire hearing (1999). The main issues raised in the voir dire hearing were 1. Contamination, 2. Heteroplasmy, 3. Science still debated in terms of recombination and paternal inheritance. - The eukaryotic cell and mitochondria: In the cell DNA is found in the nucleus and the mitochondria. The mitochondria are responsible for energy production and most of its genes are used for this function. In each cell there are hundreds to thousands of mitochondria, which means a high copy number. Within a mitochondrion there are at least two genomes. This plus the fact that there are many mitochondria per cell, means there is a high copy number per cell. There are lots of targets for primers when sequencing. This high copy number is a major reason for the use of mitochondrial DNA in special cases and in ancient DNA research. mtDNA has a helical structure, just like nuclear DNA. The mitochondrial genome accumulates lots of mutations with age, and this is an important issue in forensics. - Mitochondrial genome: The CRS focused on the light strand of the mtDNA genome. The genome is composed of 16,569 bases, which is about 0.1% of all human DNA. This is one reason they focused on sequencing it first instead of the nuclear DNA genome. The genome contains the information for the synthesis of 13 proteins, 22 tRNAs, and 12 ribosomal RNAs. These coding genes are mostly found on the heavy strand. The light strand is C/T rich and the heavy strand is G/A rich. The genome has a circular configuration. It is not a chromosome, but it is often called the 47 chromosome. There aretwo main regions of the genome used in ancient DNA and forensic work 1. D-loop or hypervariable region containing HV1 and HV2, 2. Coding region. There are two main approaches restriction enzymes define haplogroups for ethnic studies in the coding region and direct sequencing of HV1 and HV2. - Division of the mtDNA: The human mt genome is divided into coding and non-coding regions. The non-coding region, also called the displacement or D-loop region, contains two areas that are characterized by high mutation rates and are referred to as hypervariable regions 1 and 2. HV1 contains bases 16024 to 16365 and HV2 contains bases 73 to 340. When the genome was first sequenced, the functions of the various components were unknown. It is likely that had the functional differences between the non-coding (D-loop) and coding (bp 341-16023) regions and the role of non-coding regions in forensics been known, the mtDNA sequence would have been started at HV1. - Advantages of mtDNA: high copy number/cell, high mutation rate in D-loop (but this rate is slow), maternal inheritance, no recombination or mixed parentage, easier statistical analysis. - High copy number: In a cell there is a single nucleus and hundreds to thousands of mitochondria. Each mitochondrion contains on average at least 2.2 genomes. This high copy number makes it much easier to obtain results on highly degraded tissues from crime or mass disaster sites. mtDNA was first used in ancient DNA research for this reason. The nucleus has two copies of each gene per cell, inherited from both parents. These are unique to individuals. Mitochondria have 1000s of copies per cell and they are maternally inherited. They are not unique to individuals. mtDNA can be obtained from hair shafts. - High mutation rate in hypervariable region: The hypervariable regions have an unusually high substitution rate, which is good for determining maternal relationships. Though the mutation rate is high (10x greater than the coding region and the nuclear DNA genome) there is usually only base change every 33 generatio
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